The Header

GFA files may contain one or multiple header lines (record type: “H”). These lines may be present in any part of the file, not necessarily at the beginning.

Although the header may consist of multiple lines, its content refers to the whole file. Therefore in Gfapy the header is accessed using a single line instance (accessible by the header property). Header lines contain only tags. If not header line is present in the Gfa, then the header line object will be empty (i.e. contain no tags).

Note that header lines cannot be connected to the Gfa as other lines (i.e. calling connect() on them raises an exception). Instead they must be merged to the existing Gfa header, using add_line on the Gfa instance.

>>> gfa.add_line("H\tnn:f:1.0") 
>>> gfa.header.nn
1.0
>>> gfapy.Line("H\tnn:f:1.0").connect(gfa)
Traceback (most recent call last):
...
gfapy.error.RuntimeError: ...

Multiple definitions of the predefined header tags

For the predefined tags (VN and TS), the presence of multiple values in different lines is an error, unless the value is the same in each instance (in which case the repeated definitions are ignored).

>>> gfa.add_line("H\tVN:Z:1.0") 
>>> gfa.add_line("H\tVN:Z:1.0") # ignored 
>>> gfa.add_line("H\tVN:Z:2.0")
Traceback (most recent call last):
...
gfapy.error.VersionError: ...

Multiple definitions of custom header tags

If the tags are present only once in the header in its entirety, the access to the tags is the same as for any other line (see the Tags chapter).

However, the specification does not forbid custom tags to be defined with different values in different header lines (which we name “multi-definition tags”). This particular case is handled in the next sections.

Reading multi-definitions tags

Reading, validating and setting the datatype of multi-definition tags is done using the same methods as for all other lines (see the Tags chapter). However, if a tag is defined multiple times on multiple H lines, reading the tag will return a list of the values on the lines. This array is an instance of the subclass gfapy.FieldArray of list.

>>> gfa.add_line("H\txx:i:1") 
>>> gfa.add_line("H\txx:i:2") 
>>> gfa.add_line("H\txx:i:3") 
>>> gfa.header.xx
gfapy.FieldArray('i',[1, 2, 3])

Setting tags

There are two possibilities to set a tag for the header. The first is the normal tag interface (using set or the tag name property). The second is to use add. The latter supports multi-definition tags, i.e. it adds the value to the previous ones (if any), instead of overwriting them.

>>> gfa = gfapy.Gfa()
>>> gfa.header.xx
>>> gfa.header.add("xx", 1)
>>> gfa.header.xx
1
>>> gfa.header.add("xx", 2)
>>> gfa.header.xx
gfapy.FieldArray('i',[1, 2])
>>> gfa.header.set("xx", 3)
>>> gfa.header.xx
3

Modifying field array values

Field arrays can be modified directly (e.g. adding new values or removing some values). After modification, the user may check if the array values remain compatible with the datatype of the tag using the validate_field`() method.

>>> gfa = gfapy.Gfa()
>>> gfa.header.xx = gfapy.FieldArray('i',[1,2,3])
>>> gfa.header.xx
gfapy.FieldArray('i',[1, 2, 3])
>>> gfa.header.validate_field("xx")
>>> gfa.header.xx.append("X")
>>> gfa.header.validate_field("xx")
Traceback (most recent call last):
...
gfapy.error.FormatError: ...

If the field array is modified using array methods which return a list or data of any other type, a field array must be constructed, setting its datatype to the value returned by calling get_datatype() on the header.

>>> gfa = gfapy.Gfa()
>>> gfa.header.xx = gfapy.FieldArray('i',[1,2,3])
>>> gfa.header.xx
gfapy.FieldArray('i',[1, 2, 3])
>>> gfa.header.xx = gfapy.FieldArray(gfa.header.get_datatype("xx"),
... list(map(lambda x: x+1, gfa.header.xx)))
>>> gfa.header.xx
gfapy.FieldArray('i',[2, 3, 4])

String representation of the header

For consistency with other line types, the string representation of the header is a single-line string, eventually non standard-compliant, if it contains multiple instances of the tag. (and when calling field_to_s() for a tag present multiple times, the output string will contain the instances of the tag, separated by tabs).

However, when the Gfa is output to file or string, the header is split into multiple H lines with single tags, so that standard-compliant GFA is output. The split header can be retrieved using the headers property of the Gfa instance.

>>> gfa = gfapy.Gfa()
>>> gfa.header.VN = "1.0"
>>> gfa.header.xx = gfapy.FieldArray('i',[1,2])
>>> gfa.header.field_to_s("xx")
'1\t2'
>>> gfa.header.field_to_s("xx", tag=True)
'xx:i:1\txx:i:2'
>>> str(gfa.header)
'H\tVN:Z:1.0\txx:i:1\txx:i:2'
>>> [str(h) for h in gfa.headers]
['H\tVN:Z:1.0', 'H\txx:i:1', 'H\txx:i:2']
>>> str(gfa)
'H\tVN:Z:1.0\nH\txx:i:1\nH\txx:i:2'