SB Screw formats - mendessoares/BuddySuite GitHub Wiki

--screw_formats, -sf

Description

Convert between BioPython supported formats. Not all conversions are well supported by BioPython, and there hasn't been much effort yet in SeqBuddy to handle the conversions that don't work. Standard formats should be fine though, like fasta, genbank, nexus, and phylip.

The 'raw' format is specific to SeqBuddy, and strip all information from the sequences (including ids and metadata). All that is returned are the sequences separated by line breaks.

Argument

Format ( str )

The desired output format. The following formats are currently officially supported, and if you encounter any errors reading or writing them, please contact the developers.

• FASTA
• GenBank
• EMBL
• SeqXML
• PHYLIP
• NEXUS
• Stockholm
• CLUSTAL

Modifier

--in_place/-i

Works the same as all other in place calls, except that the file will be given a new extension to match the new format.

Examples

Input file: Drosophila.nex

#NEXUS
begin data;
	dimensions ntax=4 nchar=315;
	format datatype=protein missing=? gap=-;
matrix
'Dme-Panxδ3' --------GFI----KIDNMVFRCHYRITAI-LFTCCIIVTANNLIGDPISCI--IPMHVINTFCWITYTYTV-----AGPGLE-K-HSYYQWVPFVLFFQGLMFYVPHWVWKM--DGKIRMITGV---DDRDRILKYFVNNT--HNGYSFYFFCELLNFINVIVNIFMVDKFLGGAFMSYGTDVLKFSNMDQD-RFDPMIEIFPRLTKCTFHKFGPSGSVQKHDTLCVLALNILNEKIYIFLWFWFIILATISGVAVLYSVVITRTIRKE----------------GDFLILHFLSQNLSTRSYSDMLQ-----
'Dme-Panxδ2' MDVFGSVKGLLKID-QVDNNVFRMHYKATVIILIAFSLLVTSRQYIGDPIDCIVEIPLGVMDTYCWIYSTFTVPEGRDVQPGSE-KYHKYYQWVCFVLFFQAILFYVPRYLWKSWEGGRLKMLVDLSVNDKDRKIVDYF-GNLNRHNFYAFFFVCEALNFVNVIGQIYFVDFFLDGEFSTYGSDVLKFTELEPDERIDPMARVFPKVTKCTFHKYGPSGSVQTHDGLCVLPLNIVNEKIYVFLWFWFIILSIMS-ISLIYRIAVAPKLRHLLLRARSRAESEVEVAIGDWFLLYQLGKNIDPLIYKEVISDLEMG
'Dme-Panxδ4' MAAVKPLSKYLQFKVHIYDAIFTLHSKVTVALLLACTFLLSSKQYFGDPIQCFGDKD---MDAFCWIYGAYLQCA---VSKVVE-NYITYYQWVVLVLLLESFVFYMPAFLWKIWEGGRLKHLCDFK--RTHRVLVNYF----ETHFRYFVYVFCEILNLSISILNFLLLDVFFGGFWGRY-----------RNALYNQWIAVFPKCAKCEY-KGGPSGSSNIYDYLCLLPLNILNEKIFAFLWIWFILAMLIS-LKFLYRLAVLYPMRLQLLRPKKHLQVALNCSFGDWFVLMRVGNNISPELFRKLLEEL---
'Dme-Panxδ1' YKLLGSLKSYLKWQIQTDNAVFRLHNSFTTVLLLTCSLIITATQYVGQPISCIVGVP-HVVNTFCWIHSTFTMPDRREVHPGVDFKYYTYYQWVCFVLFFQAMACYTPKFLWNKFEGGLMRMIVGLNITRKRDALLDYLIKHVKRHKLYA-YWACEFLCCINIIVQMYLMNRFFDGEFLSYGTNIMKLSDVPQEQRVDPMVYVFPRVTKCTFHKYGPSGSLQKHDSLCILPLNIVNEKTYVFIWFWFWILLVL--LGLVFRCIIFPKFRPRLLNASNRIPMECRLDIGDWWLIYMLGRNLDPVIYKDVMSEFQVP
;
end;

Usage example 1

$: sb Drosophila.nex -sf fasta

Output

>Dme-Panxδ3
--------GFI----KIDNMVFRCHYRITAI-LFTCCIIVTANNLIGDPISCI--IPMHV
INTFCWITYTYTV-----AGPGLE-K-HSYYQWVPFVLFFQGLMFYVPHWVWKM--DGKI
RMITGV---DDRDRILKYFVNNT--HNGYSFYFFCELLNFINVIVNIFMVDKFLGGAFMS
YGTDVLKFSNMDQD-RFDPMIEIFPRLTKCTFHKFGPSGSVQKHDTLCVLALNILNEKIY
IFLWFWFIILATISGVAVLYSVVITRTIRKE----------------GDFLILHFLSQNL
STRSYSDMLQ-----
>Dme-Panxδ2
MDVFGSVKGLLKID-QVDNNVFRMHYKATVIILIAFSLLVTSRQYIGDPIDCIVEIPLGV
MDTYCWIYSTFTVPEGRDVQPGSE-KYHKYYQWVCFVLFFQAILFYVPRYLWKSWEGGRL
KMLVDLSVNDKDRKIVDYF-GNLNRHNFYAFFFVCEALNFVNVIGQIYFVDFFLDGEFST
YGSDVLKFTELEPDERIDPMARVFPKVTKCTFHKYGPSGSVQTHDGLCVLPLNIVNEKIY
VFLWFWFIILSIMS-ISLIYRIAVAPKLRHLLLRARSRAESEVEVAIGDWFLLYQLGKNI
DPLIYKEVISDLEMG
>Dme-Panxδ4
MAAVKPLSKYLQFKVHIYDAIFTLHSKVTVALLLACTFLLSSKQYFGDPIQCFGDKD---
MDAFCWIYGAYLQCA---VSKVVE-NYITYYQWVVLVLLLESFVFYMPAFLWKIWEGGRL
KHLCDFK--RTHRVLVNYF----ETHFRYFVYVFCEILNLSISILNFLLLDVFFGGFWGR
Y-----------RNALYNQWIAVFPKCAKCEY-KGGPSGSSNIYDYLCLLPLNILNEKIF
AFLWIWFILAMLIS-LKFLYRLAVLYPMRLQLLRPKKHLQVALNCSFGDWFVLMRVGNNI
SPELFRKLLEEL---
>Dme-Panxδ1
YKLLGSLKSYLKWQIQTDNAVFRLHNSFTTVLLLTCSLIITATQYVGQPISCIVGVP-HV
VNTFCWIHSTFTMPDRREVHPGVDFKYYTYYQWVCFVLFFQAMACYTPKFLWNKFEGGLM
RMIVGLNITRKRDALLDYLIKHVKRHKLYA-YWACEFLCCINIIVQMYLMNRFFDGEFLS
YGTNIMKLSDVPQEQRVDPMVYVFPRVTKCTFHKYGPSGSLQKHDSLCILPLNIVNEKTY
VFIWFWFWILLVL--LGLVFRCIIFPKFRPRLLNASNRIPMECRLDIGDWWLIYMLGRNL
DPVIYKDVMSEFQVP

Usage example 2

$: sb Drosophila.nex -sf raw

Output

--------GFI----KIDNMVFRCHYRITAI-LFTCCIIVTANNLIGDPISCI--IPMHVINTFCWITYTYTV-----AGPGLE-K-HSYYQWVPFVLFFQGLMFYVPHWVWKM--DGKIRMITGV---DDRDRILKYFVNNT--HNGYSFYFFCELLNFINVIVNIFMVDKFLGGAFMSYGTDVLKFSNMDQD-RFDPMIEIFPRLTKCTFHKFGPSGSVQKHDTLCVLALNILNEKIYIFLWFWFIILATISGVAVLYSVVITRTIRKE----------------GDFLILHFLSQNLSTRSYSDMLQ-----

MDVFGSVKGLLKID-QVDNNVFRMHYKATVIILIAFSLLVTSRQYIGDPIDCIVEIPLGVMDTYCWIYSTFTVPEGRDVQPGSE-KYHKYYQWVCFVLFFQAILFYVPRYLWKSWEGGRLKMLVDLSVNDKDRKIVDYF-GNLNRHNFYAFFFVCEALNFVNVIGQIYFVDFFLDGEFSTYGSDVLKFTELEPDERIDPMARVFPKVTKCTFHKYGPSGSVQTHDGLCVLPLNIVNEKIYVFLWFWFIILSIMS-ISLIYRIAVAPKLRHLLLRARSRAESEVEVAIGDWFLLYQLGKNIDPLIYKEVISDLEMG

MAAVKPLSKYLQFKVHIYDAIFTLHSKVTVALLLACTFLLSSKQYFGDPIQCFGDKD---MDAFCWIYGAYLQCA---VSKVVE-NYITYYQWVVLVLLLESFVFYMPAFLWKIWEGGRLKHLCDFK--RTHRVLVNYF----ETHFRYFVYVFCEILNLSISILNFLLLDVFFGGFWGRY-----------RNALYNQWIAVFPKCAKCEY-KGGPSGSSNIYDYLCLLPLNILNEKIFAFLWIWFILAMLIS-LKFLYRLAVLYPMRLQLLRPKKHLQVALNCSFGDWFVLMRVGNNISPELFRKLLEEL---

YKLLGSLKSYLKWQIQTDNAVFRLHNSFTTVLLLTCSLIITATQYVGQPISCIVGVP-HVVNTFCWIHSTFTMPDRREVHPGVDFKYYTYYQWVCFVLFFQAMACYTPKFLWNKFEGGLMRMIVGLNITRKRDALLDYLIKHVKRHKLYA-YWACEFLCCINIIVQMYLMNRFFDGEFLSYGTNIMKLSDVPQEQRVDPMVYVFPRVTKCTFHKYGPSGSLQKHDSLCILPLNIVNEKTYVFIWFWFWILLVL--LGLVFRCIIFPKFRPRLLNASNRIPMECRLDIGDWWLIYMLGRNLDPVIYKDVMSEFQVP

Usage example 3

$: sb Drosophila.nex -sf gb -i

Output

File over-written at:
/home/Documents/BuddySuite/workshop/test_files/Drosophila.gb