EXTRACTFEAT(1e)

📦 version 6.6.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

✨ EXTRACTFEAT ✨

okay bestie, welcome to the EMBOSS Manual for Debian section 1e page for extractfeat, and honestly? it's giving "let me pull the little annotated bits out of your sequences and hand them to you on a platter". 💅

🌸 NAME 🌸

extractfeat — extract features from sequence(s) 🧚

🎀 SYNOPSIS 🎀

extractfeat -sequence seqall [-before integer] [-after integer]
            [-source string] [-type string] [-sense integer]
            [-minscore float] [-maxscore float] [-tag string]
            [-value string] [-join boolean] [-featinname boolean]
            [-describe string] -outseq seqout

extractfeat -help

💖 DESCRIPTION 💖

extractfeat is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). no cap, that's literally the whole suite. it hangs out in the "Edit,Feature tables" command group(s), which is exactly the vibe you'd expect. 🦋

✨ OPTIONS ✨

💜 Input section

  • -sequence seqall — the sequence(s) you're feeding in, bestie. the main character of the input. 👑

🌈 Additional section

  • -before integer — if this value is greater than 0 then that number of bases or residues before the feature are included in the extracted sequence. this lets you grab the context of the feature, iykyk. if this value is negative then the start of the extracted sequence will be this number of bases/residues before the end of the feature. so a value of '10' will start the extraction 10 bases/residues before the start of the sequence, and a value of '-10' will start the extraction 10 bases/residues before the end of the feature. the output sequence will be padded with 'N' or 'X' characters if the sequence starts after the required start of the extraction. 💀 (the padding really said "not me improvising")
  • -after integer — if this value is greater than 0 then that number of bases or residues after the feature are included in the extracted sequence. again: context, we love her. if this value is negative then the end of the extracted sequence will be this number of bases/residues after the start of the feature. so a value of '10' will end the extraction 10 bases/residues after the end of the sequence, and a value of '-10' will end the extraction 10 bases/residues after the start of the feature. the output sequence will be padded with 'N' or 'X' characters if the sequence ends before the required end of the extraction. 🌸
  • -source string — by default any feature source in the feature table is shown. you can set this to match any feature source you wish to show. the source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from. the source may be wildcarded by using '*'. if you wish to show more than one source, separate their names with the character '|', eg: gene* | embl. Default value: * ✨
  • -type string — by default every feature in the feature table is extracted. you can set this to be any feature type you wish to extract. see http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types, and see the Uniprot user manual in http://www.uniprot.org/manual/sequence_annotation for a list of the Uniprot feature types. the type may be wildcarded by using '*'. if you wish to extract more than one type, separate their names with the character '|', eg: *UTR | intron. Default value: * 🦋
  • -sense integer — by default any feature type in the feature table is extracted. you can set this to match any feature sense you wish. 0 - any sense, 1 - forward sense, -1 - reverse sense. 🔥
  • -minscore float — minimum score of feature to extract (see also maxscore). Default value: 0.0
  • -maxscore float — maximum score of feature to extract. if both minscore and maxscore are zero (the default), then any score is ignored. Default value: 0.0 🙈
  • -tag string — tags are the types of extra values that a feature may have. for example in the EMBL feature table, a 'CDS' type of feature may have the tags /codon, /codon_start, /db_xref, /EC_number, /evidence, /exception, /function, /gene, /label, /map, /note, /number, /partial, /product, /protein_id, /pseudo, /standard_name, /translation, /transl_except, /transl_table, or /usedin. some of these tags also have values, for example /gene can have the value of the gene name. by default any feature tag in the feature table is extracted. you can set this to match any feature tag you wish to show. the tag may be wildcarded by using '*'. if you wish to extract more than one tag, separate their names with the character '|', eg: gene | label. Default value: * 💖
  • -value string — tag values are the values associated with a feature tag. tags are the types of extra values that a feature may have. for example in the EMBL feature table, a 'CDS' type of feature may have the tags /codon, /codon_start, /db_xref, /EC_number, /evidence, /exception, /function, /gene, /label, /map, /note, /number, /partial, /product, /protein_id, /pseudo, /standard_name, /translation, /transl_except, /transl_table, or /usedin. only some of these tags can have values, for example /gene can have the value of the gene name. by default any feature tag value in the feature table is shown. you can set this to match any feature tag value you wish to show. the tag value may be wildcarded by using '*'. if you wish to show more than one tag value, separate their names with a space or the character '|', eg: pax* | 10. Default value: * 🌟

🫶 Output section

  • -join boolean — some features, such as CDS (coding sequence) and mRNA, are composed of introns concatenated together. there may be other forms of 'joined' sequence, depending on the feature table. if this option is set TRUE, then any group of these features will be output as a single sequence. if the 'before' and 'after' qualifiers have been set, then only the sequence before the first feature and after the last feature are added. Default value: N ✨
  • -featinname boolean — to aid you in identifying the type of feature that has been output, the type of feature is added to the start of the description of the output sequence. sometimes the description of a sequence is lost in subsequent processing of the sequences file, so it is useful for the type to be a part of the sequence ID name. if you set this to be TRUE then the name is added to the ID name of the output sequence. Default value: N 👑
  • -describe string — to aid you in identifying some further properties of a feature that has been output, this lets you specify one or more tag names that should be added to the output sequence Description text, together with their values (if any). for example, if this is set to be 'gene', then if any output feature has the tag (for example) /gene=BRCA1 associated with it, then the text (gene=BRCA1) will be added to the Description line. tags are the types of extra values that a feature may have. for example in the EMBL feature table, a 'CDS' type of feature may have the tags /codon, /codon_start, /db_xref, /EC_number, /evidence, /exception, /function, /gene, /label, /map, /note, /number, /partial, /product, /protein_id, /pseudo, /standard_name, /translation, /transl_except, /transl_table, or /usedin. some of these tags also have values, for example /gene can have the value of the gene name. by default no feature tag is displayed. you can set this to match any feature tag you wish to show. the tag may be wildcarded by using '*'. if you wish to extract more than one tag, separate their names with the character '|', eg: gene | label 🎀
  • -outseq seqout — where the extracted sequences land. the final destination, bestie. 💅

💀 BUGS 💀

bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031). fr fr, they wanna hear it. 🫶

🔍 SEE ALSO 🔍

extractfeat is fully documented via the tfm(1) system. go read the whole thing, it's iconic. ⭐

👑 AUTHOR 👑

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

  • wrote the script used to autogenerate this manual page. 🛠️

this manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. it can be redistributed under the same terms as EMBOSS itself. periodt. 💖

and that's the whole page, bestie — this is EMBOSS version 6.4.0, dated 05/11/2012, and it lives in section 1e of the EMBOSS Manual for Debian. slay, go extract some features. 🦋✨
📦 where this page comes from