get_sequence and chromosome name

[dputhier]

Hi @fafa13 ,
In the get_sequence function, the chromosome names that are returned may contain additional information. Indeed, in the following case the string following " " (dna_sm:chromo...) should be discarded. Indeed, this information won't be present in the names of the chromosomes found in GTF files. Would it be possible to update this in the library ?
Best

	>1 dna_sm:chromosome chromosome:TAIR10:1:1:30427671:1 REF
	ccctaaaccctaaaccctaaaccctaaacctctgaatccttaatccctaaatccctaaat
	ctttaaatcctacatccatgaatccctaaatacctaattccctaaacccgaaaccGGTTT
	CTCTGGTTGAAAATCATTGTGTATATAATGATAATTTTATCGTTTTTATGTAATTGCTTA
	TTGTTGTGTGTAGATTTTTTAAAAATATCATTTGAGGTCAATACAAATCCTATTTCTTGT
	GGTTTTCTTTCCTTCACTTAGCTATGGATGGTTTATCTTCATTTGTTATATTGGATACAA
	GCTTTGCTACGATCTACATTTGGGAATGTGAGTCTCTTATTGTAACCTTAGGGTTGGTTT

Should be:

Hi @fafa13 ,
In the get_sequence function, the chromosome names that are returned may contain additional information. Indeed, in the following case the string following " " (dna_sm:chromo...) should be discarded. Indeed, this information won't be present in the names of the chromosomes found in GTF files. Would it be possible to update this in the library ?
Best

	>1
	ccctaaaccctaaaccctaaaccctaaacctctgaatccttaatccctaaatccctaaat
	ctttaaatcctacatccatgaatccctaaatacctaattccctaaacccgaaaccGGTTT
	CTCTGGTTGAAAATCATTGTGTATATAATGATAATTTTATCGTTTTTATGTAATTGCTTA
	TTGTTGTGTGTAGATTTTTTAAAAATATCATTTGAGGTCAATACAAATCCTATTTCTTGT
	GGTTTTCTTTCCTTCACTTAGCTATGGATGGTTTATCTTCATTTGTTATATTGGATACAA
	GCTTTGCTACGATCTACATTTGGGAATGTGAGTCTCTTATTGTAACCTTAGGGTTGGTTT

[dputhier]

See dputhier/pygtftk#171